Starting phenix.real_space_refine on Sat May 10 21:04:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iwt_35779/05_2025/8iwt_35779.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iwt_35779/05_2025/8iwt_35779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iwt_35779/05_2025/8iwt_35779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iwt_35779/05_2025/8iwt_35779.map" model { file = "/net/cci-nas-00/data/ceres_data/8iwt_35779/05_2025/8iwt_35779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iwt_35779/05_2025/8iwt_35779.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 52 5.16 5 Be 1 3.05 5 C 4345 2.51 5 N 1137 2.21 5 O 1281 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6820 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 891, 6815 Classifications: {'peptide': 891} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 35, 'TRANS': 855} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.97, per 1000 atoms: 0.73 Number of scatterers: 6820 At special positions: 0 Unit cell: (91.56, 94.08, 126.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 52 16.00 Mg 1 11.99 F 3 9.00 O 1281 8.00 N 1137 7.00 C 4345 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 1.1 seconds 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1660 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 7 sheets defined 56.7% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 22 through 29 Processing helix chain 'A' and resid 30 through 39 Processing helix chain 'A' and resid 47 through 59 removed outlier: 3.824A pdb=" N PHE A 57 " --> pdb=" O HIS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 80 removed outlier: 3.540A pdb=" N LYS A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 97 removed outlier: 3.632A pdb=" N MET A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 132 Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 235 through 238 removed outlier: 3.681A pdb=" N ASN A 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 235 through 238' Processing helix chain 'A' and resid 239 through 249 removed outlier: 3.891A pdb=" N VAL A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE A 245 " --> pdb=" O PHE A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 288 Processing helix chain 'A' and resid 290 through 305 removed outlier: 3.594A pdb=" N MET A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 328 removed outlier: 4.321A pdb=" N ILE A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 343 Processing helix chain 'A' and resid 398 through 411 Processing helix chain 'A' and resid 424 through 437 Processing helix chain 'A' and resid 439 through 444 removed outlier: 4.311A pdb=" N GLN A 443 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 489 removed outlier: 3.690A pdb=" N LYS A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR A 489 " --> pdb=" O GLN A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 520 Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 596 through 602 removed outlier: 3.740A pdb=" N MET A 602 " --> pdb=" O GLU A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 611 Processing helix chain 'A' and resid 621 through 635 removed outlier: 3.673A pdb=" N ASN A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 655 Processing helix chain 'A' and resid 666 through 673 Processing helix chain 'A' and resid 682 through 723 removed outlier: 3.703A pdb=" N MET A 723 " --> pdb=" O LEU A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 742 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 772 through 800 Processing helix chain 'A' and resid 805 through 826 Processing helix chain 'A' and resid 832 through 836 removed outlier: 3.504A pdb=" N GLU A 835 " --> pdb=" O SER A 832 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE A 836 " --> pdb=" O VAL A 833 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 832 through 836' Processing helix chain 'A' and resid 841 through 861 Processing helix chain 'A' and resid 861 through 869 Processing helix chain 'A' and resid 874 through 885 Processing helix chain 'A' and resid 886 through 905 removed outlier: 3.573A pdb=" N LYS A 904 " --> pdb=" O ARG A 900 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 146 through 151 removed outlier: 3.863A pdb=" N CYS A 141 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N HIS A 140 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N THR A 160 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 222 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER A 182 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY A 226 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ASP A 180 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ALA A 228 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA A 178 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLY A 230 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE A 176 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL A 232 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ARG A 174 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY A 234 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP A 172 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 151 removed outlier: 3.863A pdb=" N CYS A 141 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N HIS A 140 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N THR A 160 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 222 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER A 182 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY A 226 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ASP A 180 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ALA A 228 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA A 178 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLY A 230 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE A 176 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL A 232 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ARG A 174 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY A 234 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP A 172 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 330 through 332 Processing sheet with id=AA4, first strand: chain 'A' and resid 593 through 595 removed outlier: 8.691A pdb=" N PHE A 617 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N MET A 568 " --> pdb=" O PHE A 617 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 393 removed outlier: 4.694A pdb=" N VAL A 386 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N VAL A 362 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A 545 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS A 364 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU A 527 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU A 541 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU A 525 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY A 543 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG A 523 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 476 " --> pdb=" O CYS A 465 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL A 466 " --> pdb=" O ARG A 448 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG A 448 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 391 through 393 removed outlier: 4.694A pdb=" N VAL A 386 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N VAL A 362 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A 545 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS A 364 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N CYS A 490 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE A 538 " --> pdb=" O CYS A 490 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR A 492 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N GLY A 540 " --> pdb=" O THR A 492 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N GLN A 494 " --> pdb=" O GLY A 540 " (cutoff:3.500A) removed outlier: 13.785A pdb=" N VAL A 542 " --> pdb=" O GLN A 494 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 415 through 417 443 hydrogen bonds defined for protein. 1299 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1152 1.32 - 1.44: 1618 1.44 - 1.56: 4070 1.56 - 1.69: 3 1.69 - 1.81: 84 Bond restraints: 6927 Sorted by residual: bond pdb=" CA LYS A 351 " pdb=" C LYS A 351 " ideal model delta sigma weight residual 1.525 1.467 0.059 1.02e-02 9.61e+03 3.30e+01 bond pdb=" F2 BEF A1001 " pdb="BE BEF A1001 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" CA SER A 901 " pdb=" C SER A 901 " ideal model delta sigma weight residual 1.524 1.473 0.051 1.24e-02 6.50e+03 1.71e+01 bond pdb=" F3 BEF A1001 " pdb="BE BEF A1001 " ideal model delta sigma weight residual 1.476 1.543 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" CA THR A 352 " pdb=" C THR A 352 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.34e-02 5.57e+03 1.03e+01 ... (remaining 6922 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 9296 2.75 - 5.50: 72 5.50 - 8.25: 9 8.25 - 11.00: 1 11.00 - 13.75: 2 Bond angle restraints: 9380 Sorted by residual: angle pdb=" N ASP A 350 " pdb=" CA ASP A 350 " pdb=" C ASP A 350 " ideal model delta sigma weight residual 110.53 97.72 12.81 1.29e+00 6.01e-01 9.86e+01 angle pdb=" N SER A 901 " pdb=" CA SER A 901 " pdb=" C SER A 901 " ideal model delta sigma weight residual 110.97 104.48 6.49 1.09e+00 8.42e-01 3.55e+01 angle pdb=" F2 BEF A1001 " pdb="BE BEF A1001 " pdb=" F3 BEF A1001 " ideal model delta sigma weight residual 119.96 106.21 13.75 3.00e+00 1.11e-01 2.10e+01 angle pdb=" N ILE A 233 " pdb=" CA ILE A 233 " pdb=" C ILE A 233 " ideal model delta sigma weight residual 113.53 109.48 4.05 9.80e-01 1.04e+00 1.71e+01 angle pdb=" N PRO A 805 " pdb=" CA PRO A 805 " pdb=" C PRO A 805 " ideal model delta sigma weight residual 112.47 120.59 -8.12 2.06e+00 2.36e-01 1.55e+01 ... (remaining 9375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 3622 16.92 - 33.84: 450 33.84 - 50.76: 130 50.76 - 67.68: 21 67.68 - 84.60: 9 Dihedral angle restraints: 4232 sinusoidal: 1666 harmonic: 2566 Sorted by residual: dihedral pdb=" CA ASP A 757 " pdb=" CB ASP A 757 " pdb=" CG ASP A 757 " pdb=" OD1 ASP A 757 " ideal model delta sinusoidal sigma weight residual -30.00 -88.42 58.42 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CG ARG A 403 " pdb=" CD ARG A 403 " pdb=" NE ARG A 403 " pdb=" CZ ARG A 403 " ideal model delta sinusoidal sigma weight residual -180.00 -137.43 -42.57 2 1.50e+01 4.44e-03 9.76e+00 dihedral pdb=" CA LYS A 327 " pdb=" CB LYS A 327 " pdb=" CG LYS A 327 " pdb=" CD LYS A 327 " ideal model delta sinusoidal sigma weight residual 180.00 120.42 59.58 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 945 0.054 - 0.108: 165 0.108 - 0.162: 14 0.162 - 0.217: 3 0.217 - 0.271: 2 Chirality restraints: 1129 Sorted by residual: chirality pdb=" CA PRO A 805 " pdb=" N PRO A 805 " pdb=" C PRO A 805 " pdb=" CB PRO A 805 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CB ILE A 784 " pdb=" CA ILE A 784 " pdb=" CG1 ILE A 784 " pdb=" CG2 ILE A 784 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB ILE A 18 " pdb=" CA ILE A 18 " pdb=" CG1 ILE A 18 " pdb=" CG2 ILE A 18 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1126 not shown) Planarity restraints: 1185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 804 " -0.079 5.00e-02 4.00e+02 1.19e-01 2.28e+01 pdb=" N PRO A 805 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO A 805 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO A 805 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 253 " -0.045 5.00e-02 4.00e+02 6.73e-02 7.24e+00 pdb=" N PRO A 254 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 254 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 254 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 452 " -0.039 5.00e-02 4.00e+02 5.76e-02 5.30e+00 pdb=" N PRO A 453 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 453 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 453 " -0.032 5.00e-02 4.00e+02 ... (remaining 1182 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 13 2.33 - 2.97: 3241 2.97 - 3.61: 10229 3.61 - 4.26: 14798 4.26 - 4.90: 25505 Nonbonded interactions: 53786 Sorted by model distance: nonbonded pdb=" OD2 ASP A 350 " pdb=" F1 BEF A1001 " model vdw 1.687 2.990 nonbonded pdb=" F1 BEF A1001 " pdb="MG MG A1002 " model vdw 1.757 2.120 nonbonded pdb=" OD2 ASP A 350 " pdb="BE BEF A1001 " model vdw 1.815 1.936 nonbonded pdb=" OD1 ASP A 644 " pdb="MG MG A1002 " model vdw 2.071 2.170 nonbonded pdb=" OD2 ASP A 350 " pdb="MG MG A1002 " model vdw 2.104 2.170 ... (remaining 53781 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 20.200 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.789 6928 Z= 0.973 Angle : 0.633 13.749 9380 Z= 0.371 Chirality : 0.041 0.271 1129 Planarity : 0.006 0.119 1185 Dihedral : 16.196 84.605 2572 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.70 % Favored : 96.96 % Rotamer: Outliers : 0.52 % Allowed : 23.27 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.30), residues: 889 helix: 2.56 (0.23), residues: 510 sheet: 0.43 (0.53), residues: 101 loop : 0.46 (0.41), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 460 HIS 0.002 0.000 HIS A 149 PHE 0.019 0.001 PHE A 57 TYR 0.007 0.001 TYR A 510 ARG 0.007 0.000 ARG A 760 Details of bonding type rmsd hydrogen bonds : bond 0.14529 ( 419) hydrogen bonds : angle 5.63873 ( 1299) covalent geometry : bond 0.00394 ( 6927) covalent geometry : angle 0.63273 ( 9380) Misc. bond : bond 0.78865 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.710 Fit side-chains REVERT: A 57 PHE cc_start: 0.7653 (t80) cc_final: 0.7334 (t80) outliers start: 4 outliers final: 1 residues processed: 110 average time/residue: 0.1914 time to fit residues: 28.0753 Evaluate side-chains 102 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 901 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 37 optimal weight: 0.0270 chunk 23 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.172625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.149015 restraints weight = 7851.296| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 1.71 r_work: 0.3718 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 6928 Z= 0.133 Angle : 0.521 9.575 9380 Z= 0.275 Chirality : 0.042 0.307 1129 Planarity : 0.006 0.126 1185 Dihedral : 3.610 17.887 940 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.59 % Favored : 97.19 % Rotamer: Outliers : 2.48 % Allowed : 20.92 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.29), residues: 889 helix: 2.69 (0.23), residues: 493 sheet: 0.51 (0.51), residues: 107 loop : 0.30 (0.40), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 60 HIS 0.002 0.001 HIS A 394 PHE 0.009 0.001 PHE A 176 TYR 0.008 0.001 TYR A 272 ARG 0.005 0.001 ARG A 55 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 419) hydrogen bonds : angle 4.13654 ( 1299) covalent geometry : bond 0.00311 ( 6927) covalent geometry : angle 0.52063 ( 9380) Misc. bond : bond 0.00148 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.719 Fit side-chains REVERT: A 281 MET cc_start: 0.7187 (mmt) cc_final: 0.6108 (mmt) REVERT: A 402 SER cc_start: 0.8789 (m) cc_final: 0.8428 (p) REVERT: A 803 ILE cc_start: 0.3696 (OUTLIER) cc_final: 0.3254 (pt) outliers start: 19 outliers final: 9 residues processed: 125 average time/residue: 0.2147 time to fit residues: 35.2360 Evaluate side-chains 109 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 873 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 14 optimal weight: 0.0570 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.167954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.145807 restraints weight = 7724.328| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.47 r_work: 0.3444 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 6928 Z= 0.200 Angle : 0.607 9.960 9380 Z= 0.323 Chirality : 0.044 0.287 1129 Planarity : 0.006 0.131 1185 Dihedral : 4.136 19.931 939 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.92 % Favored : 96.85 % Rotamer: Outliers : 3.53 % Allowed : 20.92 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.29), residues: 889 helix: 2.23 (0.23), residues: 492 sheet: -0.09 (0.44), residues: 117 loop : 0.20 (0.41), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 285 HIS 0.004 0.001 HIS A 394 PHE 0.018 0.002 PHE A 63 TYR 0.013 0.001 TYR A 272 ARG 0.004 0.000 ARG A 760 Details of bonding type rmsd hydrogen bonds : bond 0.05600 ( 419) hydrogen bonds : angle 4.35137 ( 1299) covalent geometry : bond 0.00479 ( 6927) covalent geometry : angle 0.60662 ( 9380) Misc. bond : bond 0.00263 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.713 Fit side-chains REVERT: A 28 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7247 (mm-30) REVERT: A 369 ASP cc_start: 0.8187 (t0) cc_final: 0.7973 (t0) REVERT: A 402 SER cc_start: 0.9049 (m) cc_final: 0.8718 (p) REVERT: A 641 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.7944 (ttt) outliers start: 27 outliers final: 14 residues processed: 133 average time/residue: 0.1861 time to fit residues: 33.6061 Evaluate side-chains 116 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 873 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 84 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 29 optimal weight: 0.0770 chunk 64 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 0.4980 chunk 60 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.171310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.149606 restraints weight = 7829.535| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.48 r_work: 0.3434 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 6928 Z= 0.122 Angle : 0.536 10.485 9380 Z= 0.277 Chirality : 0.041 0.284 1129 Planarity : 0.006 0.134 1185 Dihedral : 3.836 18.537 939 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.02 % Favored : 97.75 % Rotamer: Outliers : 2.75 % Allowed : 22.75 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.29), residues: 889 helix: 2.53 (0.23), residues: 486 sheet: -0.04 (0.45), residues: 116 loop : 0.14 (0.40), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 285 HIS 0.003 0.001 HIS A 149 PHE 0.010 0.001 PHE A 176 TYR 0.010 0.001 TYR A 272 ARG 0.004 0.000 ARG A 760 Details of bonding type rmsd hydrogen bonds : bond 0.04224 ( 419) hydrogen bonds : angle 4.11954 ( 1299) covalent geometry : bond 0.00296 ( 6927) covalent geometry : angle 0.53634 ( 9380) Misc. bond : bond 0.00062 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.719 Fit side-chains REVERT: A 28 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6867 (mm-30) REVERT: A 93 ILE cc_start: 0.8206 (pt) cc_final: 0.7915 (mt) REVERT: A 281 MET cc_start: 0.6988 (mmt) cc_final: 0.6100 (mmt) REVERT: A 402 SER cc_start: 0.9031 (m) cc_final: 0.8664 (p) REVERT: A 806 ARG cc_start: 0.5892 (ttt180) cc_final: 0.5344 (ptm160) outliers start: 21 outliers final: 15 residues processed: 124 average time/residue: 0.1813 time to fit residues: 30.4149 Evaluate side-chains 119 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 873 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 39 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.167534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.147085 restraints weight = 7736.546| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.44 r_work: 0.3416 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 6928 Z= 0.153 Angle : 0.565 10.640 9380 Z= 0.294 Chirality : 0.042 0.280 1129 Planarity : 0.006 0.136 1185 Dihedral : 3.913 18.779 939 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.92 % Favored : 96.74 % Rotamer: Outliers : 3.14 % Allowed : 23.53 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.29), residues: 889 helix: 2.37 (0.23), residues: 492 sheet: 0.00 (0.45), residues: 115 loop : 0.09 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 285 HIS 0.002 0.001 HIS A 58 PHE 0.016 0.002 PHE A 57 TYR 0.010 0.001 TYR A 272 ARG 0.006 0.000 ARG A 760 Details of bonding type rmsd hydrogen bonds : bond 0.04717 ( 419) hydrogen bonds : angle 4.17773 ( 1299) covalent geometry : bond 0.00373 ( 6927) covalent geometry : angle 0.56487 ( 9380) Misc. bond : bond 0.00133 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.963 Fit side-chains REVERT: A 28 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6905 (mm-30) REVERT: A 402 SER cc_start: 0.9052 (m) cc_final: 0.8715 (p) REVERT: A 427 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7759 (mt-10) REVERT: A 806 ARG cc_start: 0.5952 (ttt180) cc_final: 0.5349 (ptm160) outliers start: 24 outliers final: 19 residues processed: 125 average time/residue: 0.1911 time to fit residues: 32.7122 Evaluate side-chains 122 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 873 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS A 78 GLN ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.165883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.145637 restraints weight = 7787.779| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.44 r_work: 0.3439 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 6928 Z= 0.162 Angle : 0.575 10.728 9380 Z= 0.299 Chirality : 0.042 0.276 1129 Planarity : 0.006 0.137 1185 Dihedral : 3.975 19.294 939 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.81 % Favored : 96.85 % Rotamer: Outliers : 3.79 % Allowed : 23.14 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.29), residues: 889 helix: 2.26 (0.23), residues: 491 sheet: -0.22 (0.43), residues: 123 loop : 0.05 (0.41), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 285 HIS 0.004 0.001 HIS A 53 PHE 0.018 0.002 PHE A 57 TYR 0.011 0.001 TYR A 272 ARG 0.005 0.000 ARG A 760 Details of bonding type rmsd hydrogen bonds : bond 0.04774 ( 419) hydrogen bonds : angle 4.21691 ( 1299) covalent geometry : bond 0.00395 ( 6927) covalent geometry : angle 0.57451 ( 9380) Misc. bond : bond 0.00117 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.760 Fit side-chains REVERT: A 28 GLU cc_start: 0.7222 (mm-30) cc_final: 0.6920 (mm-30) REVERT: A 281 MET cc_start: 0.7183 (mmt) cc_final: 0.6674 (mmt) REVERT: A 327 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7225 (mtpt) REVERT: A 402 SER cc_start: 0.9065 (m) cc_final: 0.8723 (p) REVERT: A 427 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7836 (mt-10) REVERT: A 806 ARG cc_start: 0.5929 (ttt180) cc_final: 0.5355 (ptm160) outliers start: 29 outliers final: 21 residues processed: 135 average time/residue: 0.1927 time to fit residues: 35.1843 Evaluate side-chains 125 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 873 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 86 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.153522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.130204 restraints weight = 8033.055| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.64 r_work: 0.3460 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 6928 Z= 0.139 Angle : 0.580 12.291 9380 Z= 0.297 Chirality : 0.042 0.274 1129 Planarity : 0.006 0.137 1185 Dihedral : 3.910 18.915 939 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.81 % Favored : 96.85 % Rotamer: Outliers : 3.40 % Allowed : 23.66 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.29), residues: 889 helix: 2.37 (0.23), residues: 491 sheet: -0.16 (0.43), residues: 123 loop : 0.05 (0.41), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 285 HIS 0.004 0.001 HIS A 53 PHE 0.012 0.001 PHE A 57 TYR 0.010 0.001 TYR A 272 ARG 0.005 0.000 ARG A 760 Details of bonding type rmsd hydrogen bonds : bond 0.04394 ( 419) hydrogen bonds : angle 4.14404 ( 1299) covalent geometry : bond 0.00339 ( 6927) covalent geometry : angle 0.58000 ( 9380) Misc. bond : bond 0.00077 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.758 Fit side-chains REVERT: A 53 HIS cc_start: 0.6392 (OUTLIER) cc_final: 0.5605 (t-90) REVERT: A 281 MET cc_start: 0.7164 (mmt) cc_final: 0.6728 (mmt) REVERT: A 402 SER cc_start: 0.9098 (m) cc_final: 0.8789 (p) REVERT: A 427 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7870 (mt-10) REVERT: A 536 LEU cc_start: 0.8640 (mt) cc_final: 0.8424 (mt) REVERT: A 806 ARG cc_start: 0.5930 (ttt180) cc_final: 0.5389 (ptm160) outliers start: 26 outliers final: 21 residues processed: 124 average time/residue: 0.1770 time to fit residues: 29.6973 Evaluate side-chains 120 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 873 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 40 optimal weight: 0.9980 chunk 11 optimal weight: 0.0040 chunk 17 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 31 optimal weight: 0.0040 chunk 72 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.152693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.127719 restraints weight = 8206.737| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.86 r_work: 0.3349 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 6928 Z= 0.125 Angle : 0.563 11.411 9380 Z= 0.289 Chirality : 0.042 0.273 1129 Planarity : 0.006 0.137 1185 Dihedral : 3.851 18.739 939 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.59 % Favored : 97.08 % Rotamer: Outliers : 3.66 % Allowed : 23.27 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.29), residues: 889 helix: 2.51 (0.23), residues: 487 sheet: -0.12 (0.44), residues: 124 loop : 0.03 (0.40), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 285 HIS 0.013 0.001 HIS A 53 PHE 0.011 0.001 PHE A 812 TYR 0.009 0.001 TYR A 510 ARG 0.004 0.000 ARG A 760 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 419) hydrogen bonds : angle 4.08611 ( 1299) covalent geometry : bond 0.00304 ( 6927) covalent geometry : angle 0.56308 ( 9380) Misc. bond : bond 0.00052 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.779 Fit side-chains REVERT: A 241 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7946 (t80) REVERT: A 281 MET cc_start: 0.7159 (mmt) cc_final: 0.6600 (mmt) REVERT: A 402 SER cc_start: 0.9098 (m) cc_final: 0.8744 (p) REVERT: A 427 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7897 (mt-10) REVERT: A 535 GLN cc_start: 0.8314 (mp10) cc_final: 0.7867 (mp10) REVERT: A 536 LEU cc_start: 0.8546 (mt) cc_final: 0.8315 (mt) REVERT: A 806 ARG cc_start: 0.5773 (ttt180) cc_final: 0.5204 (ptm160) REVERT: A 825 SER cc_start: 0.8083 (OUTLIER) cc_final: 0.7721 (m) outliers start: 28 outliers final: 20 residues processed: 123 average time/residue: 0.1844 time to fit residues: 30.8085 Evaluate side-chains 121 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 873 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 31 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.151947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.128439 restraints weight = 8102.272| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.66 r_work: 0.3402 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 6928 Z= 0.148 Angle : 0.578 10.972 9380 Z= 0.298 Chirality : 0.042 0.274 1129 Planarity : 0.006 0.137 1185 Dihedral : 3.938 19.214 939 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.26 % Favored : 96.40 % Rotamer: Outliers : 3.53 % Allowed : 23.92 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.29), residues: 889 helix: 2.37 (0.23), residues: 491 sheet: 0.07 (0.44), residues: 117 loop : 0.10 (0.40), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 285 HIS 0.002 0.001 HIS A 394 PHE 0.012 0.001 PHE A 812 TYR 0.010 0.001 TYR A 272 ARG 0.004 0.000 ARG A 760 Details of bonding type rmsd hydrogen bonds : bond 0.04500 ( 419) hydrogen bonds : angle 4.14965 ( 1299) covalent geometry : bond 0.00361 ( 6927) covalent geometry : angle 0.57802 ( 9380) Misc. bond : bond 0.00093 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.703 Fit side-chains REVERT: A 53 HIS cc_start: 0.6339 (OUTLIER) cc_final: 0.5492 (t-90) REVERT: A 241 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7830 (t80) REVERT: A 281 MET cc_start: 0.7362 (mmt) cc_final: 0.6992 (mmt) REVERT: A 327 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7253 (mtpt) REVERT: A 402 SER cc_start: 0.9101 (m) cc_final: 0.8785 (p) REVERT: A 427 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7888 (mt-10) REVERT: A 535 GLN cc_start: 0.8277 (mp10) cc_final: 0.7829 (mp10) REVERT: A 806 ARG cc_start: 0.5914 (ttt180) cc_final: 0.5346 (ptm160) REVERT: A 825 SER cc_start: 0.8238 (OUTLIER) cc_final: 0.7906 (m) outliers start: 27 outliers final: 20 residues processed: 124 average time/residue: 0.1916 time to fit residues: 32.4935 Evaluate side-chains 124 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 873 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 2 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 0.0670 chunk 81 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.165189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.142042 restraints weight = 7890.705| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.63 r_work: 0.3427 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 6928 Z= 0.136 Angle : 0.576 10.867 9380 Z= 0.297 Chirality : 0.043 0.315 1129 Planarity : 0.006 0.137 1185 Dihedral : 3.918 19.098 939 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.04 % Favored : 96.63 % Rotamer: Outliers : 3.27 % Allowed : 24.31 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.29), residues: 889 helix: 2.49 (0.23), residues: 487 sheet: 0.06 (0.48), residues: 108 loop : 0.08 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 285 HIS 0.004 0.001 HIS A 53 PHE 0.012 0.001 PHE A 812 TYR 0.009 0.001 TYR A 510 ARG 0.005 0.000 ARG A 900 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 419) hydrogen bonds : angle 4.14180 ( 1299) covalent geometry : bond 0.00332 ( 6927) covalent geometry : angle 0.57618 ( 9380) Misc. bond : bond 0.00069 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.787 Fit side-chains REVERT: A 241 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7844 (t80) REVERT: A 281 MET cc_start: 0.7292 (mmt) cc_final: 0.6635 (mmt) REVERT: A 327 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7219 (mtpt) REVERT: A 402 SER cc_start: 0.9089 (m) cc_final: 0.8765 (p) REVERT: A 427 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7855 (mt-10) REVERT: A 535 GLN cc_start: 0.8209 (mp10) cc_final: 0.7746 (mp10) REVERT: A 806 ARG cc_start: 0.5887 (ttt180) cc_final: 0.5317 (ptm160) REVERT: A 825 SER cc_start: 0.8205 (OUTLIER) cc_final: 0.7876 (m) REVERT: A 900 ARG cc_start: 0.6890 (ttp-170) cc_final: 0.6631 (mtm180) outliers start: 25 outliers final: 20 residues processed: 123 average time/residue: 0.1798 time to fit residues: 30.2289 Evaluate side-chains 124 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 873 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.152760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.129181 restraints weight = 8137.423| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.66 r_work: 0.3379 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 6928 Z= 0.148 Angle : 0.579 10.956 9380 Z= 0.299 Chirality : 0.043 0.308 1129 Planarity : 0.006 0.136 1185 Dihedral : 3.971 19.317 939 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.49 % Favored : 96.18 % Rotamer: Outliers : 3.40 % Allowed : 24.44 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.29), residues: 889 helix: 2.34 (0.23), residues: 493 sheet: 0.06 (0.48), residues: 107 loop : 0.14 (0.40), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 285 HIS 0.008 0.001 HIS A 53 PHE 0.012 0.001 PHE A 812 TYR 0.010 0.001 TYR A 272 ARG 0.004 0.000 ARG A 900 Details of bonding type rmsd hydrogen bonds : bond 0.04497 ( 419) hydrogen bonds : angle 4.18419 ( 1299) covalent geometry : bond 0.00362 ( 6927) covalent geometry : angle 0.57884 ( 9380) Misc. bond : bond 0.00093 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4054.74 seconds wall clock time: 71 minutes 20.15 seconds (4280.15 seconds total)